rs1405793

Variant names:

• chr3-39715025-A-C
• rs1405793

Your query was ambiguous. Multiple possible variants found:

• chr3-39715025-A-C
• chr3-39715025-A-G
• chr3-39715025-A-T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.361 in 151,982 control chromosomes in the GnomAD database, including 12,603 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.36 (12603 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.60
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.658 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.361 AC: 54823 AN: 151862 Hom.: 12557 Cov.: 32

Gnomad AFR AF: 0.664

Gnomad AMI AF: 0.196

Gnomad AMR AF: 0.262

Gnomad ASJ AF: 0.249

Gnomad EAS AF: 0.205

Gnomad SAS AF: 0.281

Gnomad FIN AF: 0.205

Gnomad MID AF: 0.263

Gnomad NFE AF: 0.251

Gnomad OTH AF: 0.326

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.361 AC: 54919 AN: 151982 Hom.: 12603 Cov.: 32 AF XY: 0.356 AC XY: 26448 AN XY: 74306

African (AFR) AF: 0.664 AC: 27497 AN: 41390

American (AMR) AF: 0.262 AC: 3999 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.249 AC: 861 AN: 3464

East Asian (EAS) AF: 0.204 AC: 1055 AN: 5170

South Asian (SAS) AF: 0.282 AC: 1356 AN: 4816

European-Finnish (FIN) AF: 0.205 AC: 2168 AN: 10592

Middle Eastern (MID) AF: 0.269 AC: 79 AN: 294

European-Non Finnish (NFE) AF: 0.251 AC: 17045 AN: 67958

Other (OTH) AF: 0.323 AC: 681 AN: 2106

Alfa AF: 0.192 Hom.: 479

Bravo AF: 0.375

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.20
DANN	Benign	0.51
PhyloP100		-1.6

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs1405793; hg19: chr3-39756516;